On a side note i changed the steps per to 200, made a big difference, 400 was noise, My final setup is below
Port 1 (0x378) Matches what I have in system settings
Kernal Speed 25000
Pin Setup
X Axis Step Pin 2, Dir Pin 3 (Dir Low) (Step Low) Step Port 1, Dir Port 1
Y Axis Step Pin 4, Dir Pin 5 (Step Low) Step Port 1, Dir Port 1
Z Axis Step Pin 6, Dir Pin 7 (Step Low) Step Port 1, Dir Port 1
Probe Port1, Pin 15, (Active Low)
Estop Port 1, Pin 10, (Active Low)
Enable Port1, Pin 14
Motor Tuning
X Axis Steps Per 200, Velocity 2000, Acc 200, Step Pulse 3, Dir Pulse 1
Y Axis Steps Per 200, Velocity 2000, Acc 200, Step Pulse 3, Dir Pulse 1
Z Axis Steps Per 200, Velocity 800, Acc 150, Step Pulse 3, Dir Pulse 1